Maybe for the time being the best thing to do is to just have the routine issue a warning message and skip writing the particular java object to the file.

The code to modify is in interpreter/octave-value.

All of the octave-value types inherit a default save_binary from ov.h.  But, generally this is overridden by the specific octave-value type.  For an example, take a look at ov-range.h and ov-range.cc and search for save_binary.  It would easy to provide prototypes for save_binary, save_ascii in ov-java.h.  The implementations of those functions in ov-java.cc would simply issue a warning and then "return true;" to allow Octave to continue saving other variables.

I came across this issue during an Octave crash, when Octave tried to save a java object into the octave-workspace:

attempting to save variables to 'octave-workspace'...
error: octave_base_value::save_binary(): wrong type argument 'octave_java'
error: called from
    dev/scripts/imaging/nna at line 147 column 9
save to 'octave-workspace' complete
octave exited with signal 11

It also happens when using save:

octave-gui:2> x = javaObject ("java.lang.StringBuffer", "Initial string");
octave-gui:3> save foo.mat x
error: octave_base_value::save_ascii(): wrong type argument 'octave_java'
warning: save: no such variable 'x'

Which does make sense, but maybe a better error message could be done.